1
|
Ferrari BDS, Lima CHDS, Albuquerque MG. Development, validation and analysis of a human profurin 3D model using comparative modeling and molecular dynamics simulations. J Biomol Struct Dyn 2024; 42:5428-5446. [PMID: 37449759 DOI: 10.1080/07391102.2023.2231546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/11/2023] [Indexed: 07/18/2023]
Abstract
The emergence of new viruses can lead to the outbreak of pandemics as occurred at the end of 2019 with the coronavirus disease (or COVID-19). The fastest way to effectively control viral infections is to develop broad-spectrum antivirals that can fight at least an entire class of viruses. Profurin, the furin precursor propeptide, is responsible for the autoactivation step which is crucial for the maturation of several viral substrates. This role makes the study of furin and profurin interactions interesting for the development of new potential broad-spectrum antivirals for the treatment against several human viral diseases. Since there is no 3D model of profurin published in the literature or deposited in a database, this work reports the development, validation and analysis of a profurin 3D model using comparative modeling and molecular dynamics. The model is available in ModelArchive at https://www.modelarchive.org/doi/10.5452/ma-ct8l7. The usage of this model will make possible further studies of molecular docking and MD simulations of the profurin-furin system, in the design of new potential broad-spectrum antivirals for the treatment against several human viral diseases.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Brenda de Souza Ferrari
- Programa de Pós-Graduação em Química (PGQu), Instituto de Química (IQ), Laboratório de Modelagem Molecular (LabMMol), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Camilo Henrique da Silva Lima
- Programa de Pós-Graduação em Química (PGQu), Instituto de Química (IQ), Laboratório de Modelagem Molecular (LabMMol), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Magaly Girão Albuquerque
- Programa de Pós-Graduação em Química (PGQu), Instituto de Química (IQ), Laboratório de Modelagem Molecular (LabMMol), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| |
Collapse
|
2
|
Dash R, Tran NN, Lee SB, Lee BH. Structural Dynamics Analysis of USP14 Activation by AKT-Mediated Phosphorylation. Cells 2024; 13:955. [PMID: 38891087 PMCID: PMC11171753 DOI: 10.3390/cells13110955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Ubiquitin-specific protease 14 (USP14), one of the three major proteasome-associated deubiquitinating enzymes (DUBs), is known to be activated by the AKT-mediated phosphorylation at Ser432. Thereby, AKT can regulate global protein degradation by controlling the ubiquitin-proteasome system (UPS). However, the exact molecular mechanism of USP14 activation by AKT phosphorylation at the atomic level remains unknown. By performing the molecular dynamics (MD) simulation of the USP14 catalytic domain at three different states (inactive, active, and USP14-ubiquitin complex), we characterized the change in structural dynamics by phosphorylation. We observed that the Ser432 phosphorylation induced substantial conformational changes of USP14 in the blocking loop (BL) region to fold it from an open loop into a β-sheet, which is critical for USP14 activation. Furthermore, phosphorylation also increased the frequency of critical hydrogen bonding and salt bridge interactions between USP14 and ubiquitin, which is essential for DUB activity. Structural dynamics insights from this study pinpoint the important local conformational landscape of USP14 by the phosphorylation event, which would be critical for understanding USP14-mediated proteasome regulation and designing future therapeutics.
Collapse
Affiliation(s)
- Raju Dash
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea; (R.D.); (N.-N.T.)
| | - Non-Nuoc Tran
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea; (R.D.); (N.-N.T.)
| | - Sung Bae Lee
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Byung-Hoon Lee
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea; (R.D.); (N.-N.T.)
| |
Collapse
|
3
|
Mitrovic D, Chen Y, Marciniak A, Delemotte L. Coevolution-Driven Method for Efficiently Simulating Conformational Changes in Proteins Reveals Molecular Details of Ligand Effects in the β2AR Receptor. J Phys Chem B 2023; 127:9891-9904. [PMID: 37947090 PMCID: PMC10683026 DOI: 10.1021/acs.jpcb.3c04897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023]
Abstract
With the advent of AI-powered structure prediction, the scientific community is inching closer to solving protein folding. An unresolved enigma, however, is to accurately, reliably, and deterministically predict alternative conformational states that are crucial for the function of, e.g., transporters, receptors, or ion channels where conformational cycling is innately coupled to protein function. Accurately discovering and exploring all conformational states of membrane proteins has been challenging due to the need to retain atomistic detail while enhancing the sampling along interesting degrees of freedom. The challenges include but are not limited to finding which degrees of freedom are relevant, how to accelerate the sampling along them, and then quantifying the populations of each micro- and macrostate. In this work, we present a methodology that finds relevant degrees of freedom by combining evolution and physics through machine learning and apply it to the conformational sampling of the β2 adrenergic receptor. In addition to predicting new conformations that are beyond the training set, we have computed free energy surfaces associated with the protein's conformational landscape. We then show that the methodology is able to quantitatively predict the effect of an array of ligands on the β2 adrenergic receptor activation through the discovery of new metastable states not present in the training set. Lastly, we also stake out the structural determinants of activation and inactivation pathway signaling through different ligands and compare them to functional experiments to validate our methodology and potentially gain further insights into the activation mechanism of the β2 adrenergic receptor.
Collapse
Affiliation(s)
- Darko Mitrovic
- Department of Applied Physics,
Science for Life Laboratory, KTH Royal Institute
of Technology, Sweden Tomtebodavägen 23, 171
65 Solna, Sweden
| | - Yue Chen
- Department of Applied Physics,
Science for Life Laboratory, KTH Royal Institute
of Technology, Sweden Tomtebodavägen 23, 171
65 Solna, Sweden
| | - Antoni Marciniak
- Department of Applied Physics,
Science for Life Laboratory, KTH Royal Institute
of Technology, Sweden Tomtebodavägen 23, 171
65 Solna, Sweden
| | - Lucie Delemotte
- Department of Applied Physics,
Science for Life Laboratory, KTH Royal Institute
of Technology, Sweden Tomtebodavägen 23, 171
65 Solna, Sweden
| |
Collapse
|
4
|
Tóth Á, Crespi V, Janaszkiewicz A, Di Meo F. Computational and structural insights into the pre- and post-hydrolysis states of bovine multidrug resistance-associated protein 1. Basic Clin Pharmacol Toxicol 2023; 133:508-525. [PMID: 37038087 DOI: 10.1111/bcpt.13871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/12/2023]
Abstract
ATP-binding cassette C-family drug membrane transporters play an important role in local pharmacokinetics, that is, drug concentration in cellular compartments. From the structural point of view, only the bovine ortholog of the multidrug resistance-associated protein 1 (bMRP1) has been resolved. We here used μs-scaled molecular dynamics simulations to investigate the structure and dynamics of the bovine multidrug resistance-associated protein 1 in pre- and post-hydrolysis functional states. The present work aims to examine the slight but likely relevant structural differences between pre- and post-hydrolysis states of outward-facing conformations as well as the interactions between the multidrug resistance-associated protein 1 and the surrounding lipid bilayer. Global conformational dynamics show unfavourable extracellular opening associated with nucleotide-binding domain dimerization indicating that the post-hydrolysis state adopts a close-cleft conformation rather than an outward-open conformation. Our present simulations also highlight persistent interactions with annular cholesterol molecules and the expected active role of lipid bilayer in the allosteric communication between distant domains of the transporter.
Collapse
Affiliation(s)
- Ágota Tóth
- Inserm UMR 1248 Pharmacology & Transplantation, Univ. Limoges, Limoges, France
| | - Veronica Crespi
- Inserm UMR 1248 Pharmacology & Transplantation, Univ. Limoges, Limoges, France
| | | | - Florent Di Meo
- Inserm UMR 1248 Pharmacology & Transplantation, Univ. Limoges, Limoges, France
| |
Collapse
|
5
|
Oladipo SD, Zamisa SJ, Badeji AA, Ejalonibu MA, Adeleke AA, Lawal IA, Henni A, Lawal MM. Ni 2+ and Cu 2+ complexes of N-(2,6-dichlorophenyl)-N-mesityl formamidine dithiocarbamate structural and functional properties as CYP3A4 potential substrates. Sci Rep 2023; 13:13414. [PMID: 37591990 PMCID: PMC10435461 DOI: 10.1038/s41598-023-39502-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/26/2023] [Indexed: 08/19/2023] Open
Abstract
Metal compounds continued to attract diverse applications due to their malleability in several capacities. In this study, we present our findings on the crystal structures and functional properties of Ni2+ and Cu2+ complexes of N'-(2,6-dichlorophenyl)-N-mesitylformamidine dithiocarbamate (L) comprising [Ni-(L)2] (1) and [Cu-(L)2] (2) with a four-coordinate metal center. We established the two complex structures through 1H and 13C nuclear magnetic resonance (NMR), elemental, and single-crystal X-ray analysis. The analyses showed that the two complexes are isomorphous, having P21/c as a space group and a unit-cell similarity index (π) of 0.002. The two complexes conform to a distorted square planar geometry around the metal centers. The calculated and experimental data, including bond lengths, angles, and NMR values, are similar. Hirshfeld surface analysis revealed the variational contribution of the different types of intermolecular contacts driven by the crystal lattice of the two solvated complexes. Our knowledge of the potential biological implication of these structures enabled us to probe the compounds as prospective CYP3A4 inhibitors. This approach mimics current trends in pharmaceutical design and biomedicine by incorporating potentially active molecules into various media to predict their biological efficacies. The simulations show appreciable binding of compounds 1 and 2 to CYP3A4 with average interaction energies of -97 and -87 kcal/mol, respectively. The protein attains at least five conformational states in the three studied models using a Gaussian Mixture Model-based clustering and free energy prediction. Electric field analysis shows the crucial residues to substrate binding at the active site, enabling CYP3A4 structure to function prediction. The predicted inhibition with these Ni2+ and Cu2+ complexes indicates that CYP3A4 overexpression in a diseased state like cancer would reduce, thereby increasing the chemotherapeutic compounds' shelf-lives for adsorption. This multidimensional study addresses various aspects of molecular metal electronics, including their application as substrate-mimicking inhibitors. The outcome would enable further research on bio-metal compounds of critical potential.
Collapse
Affiliation(s)
- Segun D Oladipo
- Department of Chemical Sciences, Olabisi Onabanjo University, P.M.B 2002, Ago-Iwoye, Nigeria.
- School of Chemistry and Physics, Westville Campus, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa.
| | - Sizwe J Zamisa
- School of Chemistry and Physics, Westville Campus, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa
| | - Abosede A Badeji
- Department of Chemical Sciences, Tai Solarin University of Education, Ogun State, Ijagun, Nigeria
| | - Murtala A Ejalonibu
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa
| | - Adesola A Adeleke
- Department of Chemical Sciences, Olabisi Onabanjo University, P.M.B 2002, Ago-Iwoye, Nigeria
| | - Isiaka A Lawal
- Faculty of Engineering and Applied Science, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2, Canada
| | - Amr Henni
- Faculty of Engineering and Applied Science, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2, Canada
| | - Monsurat M Lawal
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa.
| |
Collapse
|
6
|
Nagel D, Sartore S, Stock G. Toward a Benchmark for Markov State Models: The Folding of HP35. J Phys Chem Lett 2023; 14:6956-6967. [PMID: 37504674 DOI: 10.1021/acs.jpclett.3c01561] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Adopting a 300 μs long MD trajectory of the folding of villin headpiece (HP35) by D. E. Shaw Research, we recently constructed a Markov state model (MSM) based on inter-residue contacts. The model reproduces the folding time and predicts that the native basin and unfolded region consist of metastable substates that are structurally well-characterized. Recognizing the need to establish well-defined benchmark problems, we study to what extent and in what sense this MSM can be employed as a reference model. Hence, we test the robustness of the MSM by comparing it to models that use alternative combinations of features, dimensionality reduction methods, and clustering schemes. The study suggests some main characteristics of the folding of HP35 that should be reproduced by other competitive models. Moreover, the discussion reveals which parts of the MSM workflow matter most for the considered problem and illustrates the promises and pitfalls of state-based models for the interpretation of biomolecular simulations.
Collapse
Affiliation(s)
- Daniel Nagel
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104 Freiburg, Germany
| | - Sofia Sartore
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104 Freiburg, Germany
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
7
|
Sasmal S, McCullagh M, Hocky GM. Reaction Coordinates for Conformational Transitions Using Linear Discriminant Analysis on Positions. J Chem Theory Comput 2023; 19:4427-4435. [PMID: 37130367 PMCID: PMC10373481 DOI: 10.1021/acs.jctc.3c00051] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Indexed: 05/04/2023]
Abstract
In this work, we demonstrate that Linear Discriminant Analysis (LDA) applied to atomic positions in two different states of a biomolecule produces a good reaction coordinate between those two states. Atomic coordinates of a macromolecule are a direct representation of a macromolecular configuration, and yet, they are not used in enhanced sampling studies due to a lack of rotational and translational invariance. We resolve this issue using the technique of our prior work, whereby a molecular configuration is considered a member of an equivalence class in size-and-shape space, which is the set of all configurations that can be translated and rotated to a single point within a reference multivariate Gaussian distribution characterizing a single molecular state. The reaction coordinates produced by LDA applied to positions are shown to be good reaction coordinates both in terms of characterizing the transition between two states of a system within a long molecular dynamics (MD) simulation and also ones that allow us to readily produce free energy estimates along that reaction coordinate using enhanced sampling MD techniques.
Collapse
Affiliation(s)
- Subarna Sasmal
- Department
of Chemistry and Simons Center for Computational Physical Chemistry, New York University, New York, New York 10003, United States
| | - Martin McCullagh
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Glen M. Hocky
- Department
of Chemistry and Simons Center for Computational Physical Chemistry, New York University, New York, New York 10003, United States
| |
Collapse
|
8
|
Papadopoulos N, Nédélec A, Derenne A, Şulea TA, Pecquet C, Chachoua I, Vertenoeil G, Tilmant T, Petrescu AJ, Mazzucchelli G, Iorga BI, Vertommen D, Constantinescu SN. Oncogenic CALR mutant C-terminus mediates dual binding to the thrombopoietin receptor triggering complex dimerization and activation. Nat Commun 2023; 14:1881. [PMID: 37019903 PMCID: PMC10076285 DOI: 10.1038/s41467-023-37277-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 03/04/2023] [Indexed: 04/07/2023] Open
Abstract
Calreticulin (CALR) frameshift mutations represent the second cause of myeloproliferative neoplasms (MPN). In healthy cells, CALR transiently and non-specifically interacts with immature N-glycosylated proteins through its N-terminal domain. Conversely, CALR frameshift mutants turn into rogue cytokines by stably and specifically interacting with the Thrombopoietin Receptor (TpoR), inducing its constitutive activation. Here, we identify the basis of the acquired specificity of CALR mutants for TpoR and define the mechanisms by which complex formation triggers TpoR dimerization and activation. Our work reveals that CALR mutant C-terminus unmasks CALR N-terminal domain, rendering it more accessible to bind immature N-glycans on TpoR. We further find that the basic mutant C-terminus is partially α-helical and define how its α-helical segment concomitantly binds acidic patches of TpoR extracellular domain and induces dimerization of both CALR mutant and TpoR. Finally, we propose a model of the tetrameric TpoR-CALR mutant complex and identify potentially targetable sites.
Collapse
Affiliation(s)
- Nicolas Papadopoulos
- Ludwig Institute for Cancer Research Brussels, Brussels, Belgium
- Université catholique de Louvain and de Duve Institute, Brussels, Belgium
| | - Audrey Nédélec
- Ludwig Institute for Cancer Research Brussels, Brussels, Belgium
- Université catholique de Louvain and de Duve Institute, Brussels, Belgium
| | - Allison Derenne
- Spectralys Biotech SRL, rue Auguste Piccard 48, 6041, Gosselies, Belgium
| | - Teodor Asvadur Şulea
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, Bucharest, 060031, Romania
| | - Christian Pecquet
- Ludwig Institute for Cancer Research Brussels, Brussels, Belgium
- Université catholique de Louvain and de Duve Institute, Brussels, Belgium
| | - Ilyas Chachoua
- Ludwig Institute for Cancer Research Brussels, Brussels, Belgium
- Université catholique de Louvain and de Duve Institute, Brussels, Belgium
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Gaëlle Vertenoeil
- Ludwig Institute for Cancer Research Brussels, Brussels, Belgium
- Université catholique de Louvain and de Duve Institute, Brussels, Belgium
| | - Thomas Tilmant
- Mass Spectrometry Laboratory, MolSys Research Unit, Universiy of Liège, 4000, Liège, Belgium
| | - Andrei-Jose Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, Bucharest, 060031, Romania
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, Universiy of Liège, 4000, Liège, Belgium
| | - Bogdan I Iorga
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, Gif-sur-Yvette, France
| | - Didier Vertommen
- Université catholique de Louvain and de Duve Institute, Brussels, Belgium
- de Duve Institute and MASSPROT platform, Brussels, Belgium
| | - Stefan N Constantinescu
- Ludwig Institute for Cancer Research Brussels, Brussels, Belgium.
- Université catholique de Louvain and de Duve Institute, Brussels, Belgium.
- Walloon Excelence in Life Sciences and Biotechnology, WELBIO, avenue Pasteur, 6, 1300, Wavre, Belgium.
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, Oxford University, Oxford, UK.
| |
Collapse
|
9
|
Kotobi A, Schwob L, Vonbun-Feldbauer GB, Rossi M, Gasparotto P, Feiler C, Berden G, Oomens J, Oostenrijk B, Scuderi D, Bari S, Meißner RH. Reconstructing the infrared spectrum of a peptide from representative conformers of the full canonical ensemble. Commun Chem 2023; 6:46. [PMID: 36869192 PMCID: PMC9984374 DOI: 10.1038/s42004-023-00835-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/08/2023] [Indexed: 03/05/2023] Open
Abstract
Leucine enkephalin (LeuEnk), a biologically active endogenous opioid pentapeptide, has been under intense investigation because it is small enough to allow efficient use of sophisticated computational methods and large enough to provide insights into low-lying minima of its conformational space. Here, we reproduce and interpret experimental infrared (IR) spectra of this model peptide in gas phase using a combination of replica-exchange molecular dynamics simulations, machine learning, and ab initio calculations. In particular, we evaluate the possibility of averaging representative structural contributions to obtain an accurate computed spectrum that accounts for the corresponding canonical ensemble of the real experimental situation. Representative conformers are identified by partitioning the conformational phase space into subensembles of similar conformers. The IR contribution of each representative conformer is calculated from ab initio and weighted according to the population of each cluster. Convergence of the averaged IR signal is rationalized by merging contributions in a hierarchical clustering and the comparison to IR multiple photon dissociation experiments. The improvements achieved by decomposing clusters containing similar conformations into even smaller subensembles is strong evidence that a thorough assessment of the conformational landscape and the associated hydrogen bonding is a prerequisite for deciphering important fingerprints in experimental spectroscopic data.
Collapse
Affiliation(s)
- Amir Kotobi
- grid.7683.a0000 0004 0492 0453Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Lucas Schwob
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
| | - Gregor B. Vonbun-Feldbauer
- grid.6884.20000 0004 0549 1777Hamburg University of Technology, Institute of Advanced Ceramics, Hamburg, Germany
| | - Mariana Rossi
- grid.469852.40000 0004 1796 3508Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Piero Gasparotto
- grid.5991.40000 0001 1090 7501Scientific Computing Division, Paul Scherrer Institute, Villigen, Switzerland
| | - Christian Feiler
- grid.24999.3f0000 0004 0541 3699Helmholtz-Zentrum Hereon, Institute of Surface Science, Geesthacht, Germany
| | - Giel Berden
- grid.5590.90000000122931605Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Nijmegen, The Netherlands
| | - Jos Oomens
- grid.5590.90000000122931605Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Nijmegen, The Netherlands
| | - Bart Oostenrijk
- grid.7683.a0000 0004 0492 0453Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany ,grid.9026.d0000 0001 2287 2617The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
| | - Debora Scuderi
- grid.503243.3Institut de Chimie Physique, CNRS UMR8000, Université Paris-Saclay, Orsay, France
| | - Sadia Bari
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany. .,The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany. .,Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
| | - Robert H. Meißner
- grid.24999.3f0000 0004 0541 3699Helmholtz-Zentrum Hereon, Institute of Surface Science, Geesthacht, Germany ,grid.6884.20000 0004 0549 1777Hamburg University of Technology, Institute of Polymers and Composites, Hamburg, Germany
| |
Collapse
|
10
|
Tóth Á, Janaszkiewicz A, Crespi V, Di Meo F. On the interplay between lipids and asymmetric dynamics of an NBS degenerate ABC transporter. Commun Biol 2023; 6:149. [PMID: 36737455 PMCID: PMC9898250 DOI: 10.1038/s42003-023-04537-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
Multidrug resistance-associated proteins are ABC C-family exporters. They are crucial in pharmacology as they transport various substrates across membranes. However, the role of the degenerate nucleotide-binding site (NBS) remains unclear likewise the interplay with the surrounding lipid environment. Here, we propose a dynamic and structural overview of MRP1 from ca. 110 μs molecular dynamics simulations. ATP binding to NBS1 is likely maintained along several transport cycles. Asymmetric NBD behaviour is ensured by lower signal transduction from NBD1 to the rest of the protein owing to the absence of ball-and-socket conformation between NBD1 and coupling helices. Even though surrounding lipids play an active role in the allosteric communication between the substrate-binding pocket and NBDs, our results suggest that lipid composition has a limited impact, mostly by affecting transport kinetics. We believe that our work can be extended to other degenerate NBS ABC proteins and provide hints for deciphering mechanistic differences among ABC transporters.
Collapse
Affiliation(s)
- Ágota Tóth
- grid.9966.00000 0001 2165 4861Inserm U1248 Pharmacology & Transplantation, ΩHealth Institute—Univ. Limoges, 2 rue du Prof. Descottes, 87000 F Limoges, France
| | - Angelika Janaszkiewicz
- grid.9966.00000 0001 2165 4861Inserm U1248 Pharmacology & Transplantation, ΩHealth Institute—Univ. Limoges, 2 rue du Prof. Descottes, 87000 F Limoges, France
| | - Veronica Crespi
- grid.9966.00000 0001 2165 4861Inserm U1248 Pharmacology & Transplantation, ΩHealth Institute—Univ. Limoges, 2 rue du Prof. Descottes, 87000 F Limoges, France
| | - Florent Di Meo
- Inserm U1248 Pharmacology & Transplantation, ΩHealth Institute-Univ. Limoges, 2 rue du Prof. Descottes, 87000 F, Limoges, France.
| |
Collapse
|
11
|
Waseem R, Singh Yadav N, Khan T, Ahmad F, Naqui Kazim S, Hassan I, Prakash A, Islam A. Molecular Basis of Structural Stability of Irisin: A Combined Molecular Dynamics Simulation and In vitro Studies for Urea-induced Denaturation. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2022.121120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
12
|
Rodríguez Serrano AF, Hsing IM. Prediction of Aptamer-Small-Molecule Interactions Using Metastable States from Multiple Independent Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:4799-4809. [PMID: 36134737 DOI: 10.1021/acs.jcim.2c00734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding aptamer-ligand interactions is necessary to rationally design aptamer-based systems. Commonly used in silico tools have proven to be accurate to predict RNA and DNA oligonucleotide tertiary structures. However, given the complexity of nucleic acids, the most thermodynamically stable conformation is not necessarily the one with the highest affinity for a specific ligand. Because many metastable states may coexist, it remains challenging to predict binding sites through molecular docking simulations using available computational pipelines. In this study, we used independent simulations to broaden the conformational diversity sampled from DNA initial models of distinct stability and assessed the binding affinity of selected metastable representative structures. In our results, utilizing multiple metastable conformations for molecular docking analysis helped identify structures favorable for ligand binding and accurately predict the binding sites. Our workflow was able to correctly identify the binding sites of the characterized adenosine monophosphate and l-argininamide aptamers. Additionally, we demonstrated that our pipeline can be used to aid the design of competition assays that are conducive to aptasensing strategies using an uncharacterized aflatoxin B1 aptamer. We foresee that this approach may help rationally design effective and truncated aptamer sequences interacting with protein biomarkers or small molecules of interest for drug design and sensor applications.
Collapse
Affiliation(s)
- Alan Fernando Rodríguez Serrano
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
| | - I-Ming Hsing
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
| |
Collapse
|
13
|
Schmidt T, Wang D, Jeon J, Schwieters CD, Clore GM. Quantitative Agreement between Conformational Substates of Holo Calcium-Loaded Calmodulin Detected by Double Electron-Electron Resonance EPR and Predicted by Molecular Dynamics Simulations. J Am Chem Soc 2022; 144:12043-12051. [PMID: 35759799 DOI: 10.1021/jacs.2c02201] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Calcium-loaded calmodulin (CaM/4Ca2+) comprises two domains that undergo rigid body reorientation from a predominantly extended conformation to a compact one upon binding target peptides. A recent replica-exchange molecular dynamics (MD) simulation on holo CaM/4Ca2+ suggested the existence of distinct structural clusters (substates) along the path from extended to compact conformers in the absence of substrates. Here, we experimentally demonstrate the existence of CaM/4Ca2+ substates trapped in local minima by three freezing/annealing regimes (slow, 40 s; intermediate, 1.5 s; fast, 0.5 ms) using pulsed Q-band double electron-electron resonance (DEER) EPR spectroscopy to measure interdomain distances between nitroxide spin-labels positioned at A17C and A128C in the N- and C-terminal domains, respectively. The DEER echo curves were directly fit to population-optimized P(r) pairwise distance distributions calculated from the coordinates of the MD clusters and compact crystal structure. DEER data on fully deuterated CaM/4Ca2+ were acquired at multiple values of the second echo period (10-35 μs) and analyzed globally to eliminate instrumental and overfitting artifacts and ensure accurate populations, peak positions, and widths. The DEER data for all three freezing regimes are quantitatively accounted for within experimental error by 5-6 distinct conformers comprising a predominantly populated extended form (60-75%) and progressively more compact states whose populations decrease as the degree of compactness increases. The shortest interdomain separation is found in the compact crystal structure, which has an occupancy of 4-6%. Thus, CaM/4Ca2+ samples high energy local minima comprising a few discrete substates of increasing compactness in a rugged energy landscape.
Collapse
Affiliation(s)
- Thomas Schmidt
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - David Wang
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Jaekyun Jeon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Charles D Schwieters
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| |
Collapse
|
14
|
Klem H, Hocky GM, McCullagh M. Size-and-Shape Space Gaussian Mixture Models for Structural Clustering of Molecular Dynamics Trajectories. J Chem Theory Comput 2022; 18:3218-3230. [PMID: 35483073 DOI: 10.1021/acs.jctc.1c01290] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Determining the optimal number and identity of structural clusters from an ensemble of molecular configurations continues to be a challenge. Recent structural clustering methods have focused on the use of internal coordinates due to the innate rotational and translational invariance of these features. The vast number of possible internal coordinates necessitates a feature space supervision step to make clustering tractable but yields a protocol that can be system type-specific. Particle positions offer an appealing alternative to internal coordinates but suffer from a lack of rotational and translational invariance, as well as a perceived insensitivity to regions of structural dissimilarity. Here, we present a method, denoted shape-GMM, that overcomes the shortcomings of particle positions using a weighted maximum likelihood alignment procedure. This alignment strategy is then built into an expectation maximization Gaussian mixture model (GMM) procedure to capture metastable states in the free-energy landscape. The resulting algorithm distinguishes between a variety of different structures, including those indistinguishable by root-mean-square displacement and pairwise distances, as demonstrated on several model systems. Shape-GMM results on an extensive simulation of the fast-folding HP35 Nle/Nle mutant protein support a four-state folding/unfolding mechanism, which is consistent with previous experimental results and provides kinetic details comparable to previous state-of-the art clustering approaches, as measured by the VAMP-2 score. Currently, training of shape-GMMs is recommended for systems (or subsystems) that can be represented by ≲200 particles and ≲100k configurations to estimate high-dimensional covariance matrices and balance computational expense. Once a shape-GMM is trained, it can be used to predict the cluster identities of millions of configurations.
Collapse
Affiliation(s)
- Heidi Klem
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Glen M Hocky
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| |
Collapse
|
15
|
Insights into the structure and function of the human organic anion transporter 1 in lipid bilayer membranes. Sci Rep 2022; 12:7057. [PMID: 35488116 PMCID: PMC9054760 DOI: 10.1038/s41598-022-10755-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/12/2022] [Indexed: 01/27/2023] Open
Abstract
The human SLC22A6/OAT1 plays an important role in the elimination of a broad range of endogenous substances and xenobiotics thus attracting attention from the pharmacological community. Furthermore, OAT1 is also involved in key physiological events such as the remote inter-organ communication. Despite its significance, the knowledge about hOAT1 structure and the transport mechanism at the atomic level remains fragmented owing to the lack of resolved structures. By means of protein-threading modeling refined by μs-scaled Molecular Dynamics simulations, the present study provides the first robust model of hOAT1 in outward-facing conformation. Taking advantage of the AlphaFold 2 predicted structure of hOAT1 in inward-facing conformation, we here provide the essential structural and functional features comparing both states. The intracellular motifs conserved among Major Facilitator Superfamily members create a so-called “charge-relay system” that works as molecular switches modulating the conformation. The principal element of the event points at interactions of charged residues that appear crucial for the transporter dynamics and function. Moreover, hOAT1 model was embedded in different lipid bilayer membranes highlighting the crucial structural dependence on lipid-protein interactions. MD simulations supported the pivotal role of phosphatidylethanolamine components to the protein conformation stability. The present model is made available to decipher the impact of any observed polymorphism and mutation on drug transport as well as to understand substrate binding modes.
Collapse
|
16
|
Human Vitamin K Epoxide Reductase as a Target of Its Redox Protein. Int J Mol Sci 2022; 23:ijms23073899. [PMID: 35409257 PMCID: PMC8998853 DOI: 10.3390/ijms23073899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 02/05/2023] Open
Abstract
Human vitamin K epoxide reductase (hVKORC1) enzymatic activity requires an initial activation by a specific redox protein, a less studied step in the hVKORC1 vital cycle. Significant steric conditions must be met by enzymes, being that to adapt their configurations is mandatory for hVKORC1 activation. We studied, by molecular dynamics (MD) simulations, the folding and conformational plasticity of hVKORC1 in its inactive (fully oxidised) state using available structures, crystallographic and from de novo modelling. According to the obtained results, hVKORC1 is a modular protein composed of the stable transmembrane domain (TMD) and intrinsically disordered luminal (L) loop, possessing the great plasticity/adaptability required to perform various steps of the activation process. The docking (HADDOCK) of Protein Disulfide Isomerase (PDI) onto different hVKORC1 conformations clearly indicated that the most interpretable solutions were found on the target closed L-loop form, a prevalent conformation of hVKORC1’s oxidised state. We also suggest that the cleaved L-loop is an appropriate entity to study hVKORC1 recognition/activation by its redox protein. Additionally, the application of hVKORC1 (membrane protein) in aqueous solution is likely to prove to be very useful in practice in either in silico studies or in vitro experiments.
Collapse
|
17
|
Sunidhi S, Sacher S, Atul, Garg P, Ray A. Elucidating the Structural Features of ABCA1 in its Heterogeneous Membrane Environment. Front Mol Biosci 2022; 8:803078. [PMID: 35155567 PMCID: PMC8830745 DOI: 10.3389/fmolb.2021.803078] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/30/2021] [Indexed: 11/17/2022] Open
Abstract
ATP Binding Cassette Transporter A1 (ABCA1) plays an integral part in Reverse Cholesterol Transport (RCT) and is critical for maintaining lipid homeostasis. One theory of lipid efflux by the transporter (alternating access) proposes that ABCA1 harbours two different conformations that provide alternating access for lipid binding and release. This is followed by sequestration via a direct interaction between ABCA1 and its partner, ApoA1. The other theory (lateral access) proposes that ABCA1 obtains lipids laterally from the membrane to form a temporary extracellular “reservoir”. This reservoir contains an isolated lipid monolayer due to the net accumulation of lipids in the exofacial leaflet. Recently, a full-length Cryo-EM structure of this 2,261-residue transmembrane protein showed its discreetly folded domains and have detected the presence of a tunnel enclosed within the extracellular domains (ECDs) but not in the TMDs, giving it an outward-facing conformation. This structure was hypothesized to substantiate the lateral access theory. Utilizing long time-scale multiple replica atomistic molecular dynamics simulations (MDS), we simulated the structure in a large heterogeneous lipid environment and found that the protein undergoes several large conformational changes in its extremities. We observed that the cavity enclosed within ATP unbound form of ABCA1 is narrow at the distal ends of TMD as well as the ECD region substantiating the “lateral access” theory. We have also characterized ABCA1 and the lipid dynamics along with the protein-lipid interactions in the heterogeneous environment, providing novel insights into understanding ABCA1 conformation at an atomistic level.
Collapse
|
18
|
Ghorbani M, Prasad S, Klauda JB, Brooks BR. Variational embedding of protein folding simulations using Gaussian mixture variational autoencoders. J Chem Phys 2021; 155:194108. [PMID: 34800961 DOI: 10.1063/5.0069708] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Conformational sampling of biomolecules using molecular dynamics simulations often produces a large amount of high dimensional data that makes it difficult to interpret using conventional analysis techniques. Dimensionality reduction methods are thus required to extract useful and relevant information. Here, we devise a machine learning method, Gaussian mixture variational autoencoder (GMVAE), that can simultaneously perform dimensionality reduction and clustering of biomolecular conformations in an unsupervised way. We show that GMVAE can learn a reduced representation of the free energy landscape of protein folding with highly separated clusters that correspond to the metastable states during folding. Since GMVAE uses a mixture of Gaussians as its prior, it can directly acknowledge the multi-basin nature of the protein folding free energy landscape. To make the model end-to-end differentiable, we use a Gumbel-softmax distribution. We test the model on three long-timescale protein folding trajectories and show that GMVAE embedding resembles the folding funnel with folded states down the funnel and unfolded states outside the funnel path. Additionally, we show that the latent space of GMVAE can be used for kinetic analysis and Markov state models built on this embedding produce folding and unfolding timescales that are in close agreement with other rigorous dynamical embeddings such as time independent component analysis.
Collapse
Affiliation(s)
- Mahdi Ghorbani
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, USA
| | - Samarjeet Prasad
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, USA
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, USA
| |
Collapse
|
19
|
Modeling Catalysis in Allosteric Enzymes: Capturing Conformational Consequences. Top Catal 2021; 65:165-186. [DOI: 10.1007/s11244-021-01521-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
20
|
Shu Z, Wu M, Liao J, Chen C. FSATOOL 2.0: An integrated molecular dynamics simulation and trajectory data analysis program. J Comput Chem 2021; 43:215-224. [PMID: 34751974 DOI: 10.1002/jcc.26772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 11/08/2022]
Abstract
Molecular dynamics simulation is important in the computational study of the biomolecules. In this paper, we upgrade our previous FSATOOL to version 2.0. It is no longer a plugin as before. Besides the existed enhanced sampling and Markov state model analysis module, FSATOOL 2.0 has three new features now. First, it contains a molecular dynamics simulation engine on both CPU and GPU device. The engine works with an embedded enhanced sampling module. Second, it can do the free energy calculation by various practical methods, including the weighted histogram analysis method and Gaussian mixture model. Third, it has many subroutines to process the trajectory data, such as principal component analysis, time-structure based independent component analysis, contact analysis, and Φ-value analysis. Most importantly, all these calculations are integrated into one package. The trajectory data format is compatible with all the modules. With a proper input parameter file, users can do the molecular dynamics simulation and data analysis work by only a few simplified commands. The capabilities and theoretical backgrounds of FSATOOL 2.0 are introduced in the paper.
Collapse
Affiliation(s)
- Zirui Shu
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mincong Wu
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jun Liao
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Changjun Chen
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| |
Collapse
|
21
|
Dibrov A, Mourin M, Dibrov P, Pierce GN. Molecular dynamics modeling of the Vibrio cholera Na +-translocating NADH:quinone oxidoreductase NqrB-NqrD subunit interface. Mol Cell Biochem 2021; 477:153-165. [PMID: 34626300 PMCID: PMC8755685 DOI: 10.1007/s11010-021-04266-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/17/2021] [Indexed: 10/29/2022]
Abstract
The Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) is the major Na+ pump in aerobic pathogens such as Vibrio cholerae. The interface between two of the NQR subunits, NqrB and NqrD, has been proposed to harbor a binding site for inhibitors of Na+-NQR. While the mechanisms underlying Na+-NQR function and inhibition remain underinvestigated, their clarification would facilitate the design of compounds suitable for clinical use against pathogens containing Na+-NQR. An in silico model of the NqrB-D interface suitable for use in molecular dynamics simulations was successfully constructed. A combination of algorithmic and manual methods was used to reconstruct portions of the two subunits unresolved in the published crystal structure and validate the resulting structure. Hardware and software optimizations that improved the efficiency of the simulation were considered and tested. The geometry of the reconstructed complex compared favorably to the published V. cholerae Na+-NQR crystal structure. Results from one 1 µs, three 150 ns and two 50 ns molecular dynamics simulations illustrated the stability of the system and defined the limitations of this model. When placed in a lipid bilayer under periodic boundary conditions, the reconstructed complex was completely stable for at least 1 µs. However, the NqrB-D interface underwent a non-physiological transition after 350 ns.
Collapse
Affiliation(s)
- Alexander Dibrov
- Department of Family Medicine, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB, Canada.
| | - Muntahi Mourin
- Department of Physiology and Pathophysiology, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,Albrechtsen Research Centre, St. Boniface Hospital, 351 Taché Avenue, Winnipeg, MB, Canada
| | - Pavel Dibrov
- Department of Microbiology, Faculty of Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Grant N Pierce
- Department of Physiology and Pathophysiology, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,Albrechtsen Research Centre, St. Boniface Hospital, 351 Taché Avenue, Winnipeg, MB, Canada
| |
Collapse
|
22
|
Glielmo A, Husic BE, Rodriguez A, Clementi C, Noé F, Laio A. Unsupervised Learning Methods for Molecular Simulation Data. Chem Rev 2021; 121:9722-9758. [PMID: 33945269 PMCID: PMC8391792 DOI: 10.1021/acs.chemrev.0c01195] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Indexed: 12/21/2022]
Abstract
Unsupervised learning is becoming an essential tool to analyze the increasingly large amounts of data produced by atomistic and molecular simulations, in material science, solid state physics, biophysics, and biochemistry. In this Review, we provide a comprehensive overview of the methods of unsupervised learning that have been most commonly used to investigate simulation data and indicate likely directions for further developments in the field. In particular, we discuss feature representation of molecular systems and present state-of-the-art algorithms of dimensionality reduction, density estimation, and clustering, and kinetic models. We divide our discussion into self-contained sections, each discussing a specific method. In each section, we briefly touch upon the mathematical and algorithmic foundations of the method, highlight its strengths and limitations, and describe the specific ways in which it has been used-or can be used-to analyze molecular simulation data.
Collapse
Affiliation(s)
- Aldo Glielmo
- International
School for Advanced Studies (SISSA) 34014 Trieste, Italy
| | - Brooke E. Husic
- Freie
Universität Berlin, Department of Mathematics
and Computer Science, 14195 Berlin, Germany
| | - Alex Rodriguez
- International Centre for Theoretical
Physics (ICTP), Condensed Matter and Statistical
Physics Section, 34100 Trieste, Italy
| | - Cecilia Clementi
- Freie
Universität Berlin, Department for
Physics, 14195 Berlin, Germany
- Rice
University Houston, Department of Chemistry, Houston, Texas 77005, United States
| | - Frank Noé
- Freie
Universität Berlin, Department of Mathematics
and Computer Science, 14195 Berlin, Germany
- Freie
Universität Berlin, Department for
Physics, 14195 Berlin, Germany
- Rice
University Houston, Department of Chemistry, Houston, Texas 77005, United States
| | - Alessandro Laio
- International
School for Advanced Studies (SISSA) 34014 Trieste, Italy
- International Centre for Theoretical
Physics (ICTP), Condensed Matter and Statistical
Physics Section, 34100 Trieste, Italy
| |
Collapse
|
23
|
Cao X, Tian P. "Dividing and Conquering" and "Caching" in Molecular Modeling. Int J Mol Sci 2021; 22:5053. [PMID: 34068835 PMCID: PMC8126232 DOI: 10.3390/ijms22095053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 11/17/2022] Open
Abstract
Molecular modeling is widely utilized in subjects including but not limited to physics, chemistry, biology, materials science and engineering. Impressive progress has been made in development of theories, algorithms and software packages. To divide and conquer, and to cache intermediate results have been long standing principles in development of algorithms. Not surprisingly, most important methodological advancements in more than half century of molecular modeling are various implementations of these two fundamental principles. In the mainstream classical computational molecular science, tremendous efforts have been invested on two lines of algorithm development. The first is coarse graining, which is to represent multiple basic particles in higher resolution modeling as a single larger and softer particle in lower resolution counterpart, with resulting force fields of partial transferability at the expense of some information loss. The second is enhanced sampling, which realizes "dividing and conquering" and/or "caching" in configurational space with focus either on reaction coordinates and collective variables as in metadynamics and related algorithms, or on the transition matrix and state discretization as in Markov state models. For this line of algorithms, spatial resolution is maintained but results are not transferable. Deep learning has been utilized to realize more efficient and accurate ways of "dividing and conquering" and "caching" along these two lines of algorithmic research. We proposed and demonstrated the local free energy landscape approach, a new framework for classical computational molecular science. This framework is based on a third class of algorithm that facilitates molecular modeling through partially transferable in resolution "caching" of distributions for local clusters of molecular degrees of freedom. Differences, connections and potential interactions among these three algorithmic directions are discussed, with the hope to stimulate development of more elegant, efficient and reliable formulations and algorithms for "dividing and conquering" and "caching" in complex molecular systems.
Collapse
Affiliation(s)
- Xiaoyong Cao
- School of Life Sciences, Jilin University, Changchun 130012, China;
| | - Pu Tian
- School of Life Sciences, Jilin University, Changchun 130012, China;
- School of Artificial Intelligence, Jilin University, Changchun 130012, China
| |
Collapse
|
24
|
Structural resolution of switchable states of a de novo peptide assembly. Nat Commun 2021; 12:1530. [PMID: 33750792 PMCID: PMC7943578 DOI: 10.1038/s41467-021-21851-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/12/2021] [Indexed: 12/18/2022] Open
Abstract
De novo protein design is advancing rapidly. However, most designs are for single states. Here we report a de novo designed peptide that forms multiple α-helical-bundle states that are accessible and interconvertible under the same conditions. Usually in such designs amphipathic α helices associate to form compact structures with consolidated hydrophobic cores. However, recent rational and computational designs have delivered open α-helical barrels with functionalisable cavities. By placing glycine judiciously in the helical interfaces of an α-helical barrel, we obtain both open and compact states in a single protein crystal. Molecular dynamics simulations indicate a free-energy landscape with multiple and interconverting states. Together, these findings suggest a frustrated system in which steric interactions that maintain the open barrel and the hydrophobic effect that drives complete collapse are traded-off. Indeed, addition of a hydrophobic co-solvent that can bind within the barrel affects the switch between the states both in silico and experimentally. So far most of the de novo designed proteins are for single states only. Here, the authors present the de novo design and crystal structure determination of a coiled-coil peptide that assembles into multiple, distinct conformational states under the same conditions and further characterise its properties with biophysical experiments, NMR and MD simulations.
Collapse
|
25
|
Kang PW, Westerlund AM, Shi J, White KM, Dou AK, Cui AH, Silva JR, Delemotte L, Cui J. Calmodulin acts as a state-dependent switch to control a cardiac potassium channel opening. SCIENCE ADVANCES 2020; 6:6/50/eabd6798. [PMID: 33310856 PMCID: PMC7732179 DOI: 10.1126/sciadv.abd6798] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/27/2020] [Indexed: 05/09/2023]
Abstract
Calmodulin (CaM) and phosphatidylinositol 4,5-bisphosphate (PIP2) are potent regulators of the voltage-gated potassium channel KCNQ1 (KV7.1), which conducts the cardiac I Ks current. Although cryo-electron microscopy structures revealed intricate interactions between the KCNQ1 voltage-sensing domain (VSD), CaM, and PIP2, the functional consequences of these interactions remain unknown. Here, we show that CaM-VSD interactions act as a state-dependent switch to control KCNQ1 pore opening. Combined electrophysiology and molecular dynamics network analysis suggest that VSD transition into the fully activated state allows PIP2 to compete with CaM for binding to VSD. This leads to conformational changes that alter VSD-pore coupling to stabilize open states. We identify a motif in the KCNQ1 cytosolic domain, which works downstream of CaM-VSD interactions to facilitate the conformational change. Our findings suggest a gating mechanism that integrates PIP2 and CaM in KCNQ1 voltage-dependent activation, yielding insights into how KCNQ1 gains the phenotypes critical for its physiological function.
Collapse
Affiliation(s)
- Po Wei Kang
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University, St. Louis, MO 63130, USA
| | - Annie M Westerlund
- Department of Applied Physics, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Jingyi Shi
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University, St. Louis, MO 63130, USA
| | - Kelli McFarland White
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University, St. Louis, MO 63130, USA
| | - Alex K Dou
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University, St. Louis, MO 63130, USA
| | - Amy H Cui
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University, St. Louis, MO 63130, USA
| | - Jonathan R Silva
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University, St. Louis, MO 63130, USA
| | - Lucie Delemotte
- Department of Applied Physics, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden.
| | - Jianmin Cui
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University, St. Louis, MO 63130, USA.
| |
Collapse
|
26
|
Mhashal AR, Romero-Rivera A, Mydy LS, Cristobal JR, Gulick AM, Richard JP, Kamerlin SCL. Modeling the Role of a Flexible Loop and Active Site Side Chains in Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase. ACS Catal 2020; 10:11253-11267. [PMID: 33042609 PMCID: PMC7536716 DOI: 10.1021/acscatal.0c02757] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/31/2020] [Indexed: 11/30/2022]
Abstract
![]()
Glycerol-3-phosphate
dehydrogenase is a biomedically important
enzyme that plays a crucial role in lipid biosynthesis. It is activated
by a ligand-gated conformational change that is necessary for the
enzyme to reach a catalytically competent conformation capable of
efficient transition-state stabilization. While the human form (hlGPDH) has been the subject of extensive structural and
biochemical studies, corresponding computational studies to support
and extend experimental observations have been lacking. We perform
here detailed empirical valence bond and Hamiltonian replica exchange
molecular dynamics simulations of wild-type hlGPDH
and its variants, as well as providing a crystal structure of the
binary hlGPDH·NAD R269A variant where the enzyme
is present in the open conformation. We estimated the activation free
energies for the hydride transfer reaction in wild-type and substituted hlGPDH and investigated the effect of mutations on catalysis
from a detailed structural study. In particular, the K120A and R269A
variants increase both the volume and solvent exposure of the active
site, with concomitant loss of catalytic activity. In addition, the
R269 side chain interacts with both the Q295 side chain on the catalytic
loop, and the substrate phosphodianion. Our structural data and simulations
illustrate the critical role of this side chain in facilitating the
closure of hlGPDH into a catalytically competent
conformation, through modulating the flexibility of a key catalytic
loop (292-LNGQKL-297). This, in turn, rationalizes a tremendous 41,000
fold decrease experimentally in the turnover number, kcat, upon truncating this residue, as loop closure is
essential for both correct positioning of key catalytic residues in
the active site, as well as sequestering the active site from the
solvent. Taken together, our data highlight the importance of this
ligand-gated conformational change in catalysis, a feature that can
be exploited both for protein engineering and for the design of allosteric
inhibitors targeting this biomedically important enzyme.
Collapse
Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry—BMC, Uppsala University, Box 576, Uppsala SE-751 23, Sweden
| | - Adrian Romero-Rivera
- Department of Chemistry—BMC, Uppsala University, Box 576, Uppsala SE-751 23, Sweden
| | - Lisa S. Mydy
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203-1121, United States
| | - Judith R. Cristobal
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Andrew M. Gulick
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203-1121, United States
| | - John P. Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Shina C. L. Kamerlin
- Department of Chemistry—BMC, Uppsala University, Box 576, Uppsala SE-751 23, Sweden
| |
Collapse
|